Polygenic Score (PGS) ID: PGS001345

Predicted Trait
Reported Trait Asthma (diagnosed by doctor)
Mapped Trait(s) asthma (MONDO_0004979)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN22127
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_BIN22127
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 435
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
68,835 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 8,721 cases
  • , 60,114 controls
]
 European UKB — — — white British ancestry —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM009206 PSS003676|
African Ancestry|
516 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed asthma — AUROC: 0.66261 [0.59914, 0.72609] R²: 0.07843
Incremental AUROC (full-covars): 0.01462
PGS R2 (no covariates): 0.00704
PGS AUROC (no covariates): 0.54765 [0.47414, 0.62116]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009207 PSS003677|
East Asian Ancestry|
245 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed asthma — AUROC: 0.67066 [0.56822, 0.7731] R²: 0.10676
Incremental AUROC (full-covars): 0.02219
PGS R2 (no covariates): 0.03135
PGS AUROC (no covariates): 0.60951 [0.50092, 0.71811]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009208 PSS003678|
European Ancestry|
5,959 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed asthma — AUROC: 0.59515 [0.57415, 0.61614] R²: 0.02426
Incremental AUROC (full-covars): 0.0264
PGS R2 (no covariates): 0.01031
PGS AUROC (no covariates): 0.56199 [0.54029, 0.58369]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009209 PSS003679|
South Asian Ancestry|
707 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed asthma — AUROC: 0.63251 [0.57541, 0.68961] R²: 0.04811
Incremental AUROC (full-covars): 0.0046
PGS R2 (no covariates): 0.00714
PGS AUROC (no covariates): 0.53871 [0.47553, 0.60189]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009210 PSS003680|
European Ancestry|
17,244 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Doctor diagnosed asthma — AUROC: 0.60258 [0.58999, 0.61516] R²: 0.02879
Incremental AUROC (full-covars): 0.03437
PGS R2 (no covariates): 0.01667
PGS AUROC (no covariates): 0.57923 [0.56641, 0.59204]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS003676 — —
[
  • 80 cases
  • , 436 controls
]
 — African unspecified — UKB —
PSS003677 — —
[
  • 29 cases
  • , 216 controls
]
 — East Asian — UKB —
PSS003678 — —
[
  • 793 cases
  • , 5,166 controls
]
 — European non-white British ancestry UKB —
PSS003679 — —
[
  • 99 cases
  • , 608 controls
]
 — South Asian — UKB —
PSS003680 — —
[
  • 2,213 cases
  • , 15,031 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)